CDPost                  'countData' object derived from data file
                        'simData' with estimated likelihoods of
                        differential expression.
CDPriors                'countData' object derived from data file
                        'simData' with estimated priors.
baySeq-classes          baySeq - classes
baySeq-package          Empirical Bayesian analysis of patterns of
                        differential expression in count data.
bimodalSep              A function that, given a numeric vector, finds
                        the value which splits the data into two sets
                        of minimal total variance.
getLibsizes             Estimates library scaling factors (library
                        sizes) for count data.
getLikelihoods          Finds posterior likelihoods for each count as
                        belonging to some hypothesis.
getPosteriors           An internal function in the baySeq package for
                        calculating posterior likelihoods given
                        likelihoods of the data.
getPriors               Estimates prior parameters for the underlying
                        distributions of 'count' data.
getTPs                  Gets the number of true positives in the top n
                        counts selected by ranked posterior likelihoods
mobAnnotation           Annotation data for a set of small RNA loci
                        derived from sequencing of grafts of
                        Arabidopsis thaliana intended for differential
                        expression analyses.
mobData                 Data from a set of small RNA sequencing
                        experiments carried out on grafts of
                        Arabidopsis thaliana intended for differential
                        expression analyses.
plotMA.CD               'MA'-plot for count data.
plotPosteriors          Plots the posterior likelihoods estimated for a
                        'countData' object against the log-ratios
                        observed between two sets of sample data.
plotPriors              Plots the density of the log values estimated
                        for the mean rate in the prior data for the
                        Negative Binomial approach to detecting
                        differential expression
simData                 Simulated data for testing the baySeq package
                        methods; simulated counts and library sizes
                        from a pairwise differential expression
                        analysis.
topCounts               Get the top counts corresponding to some group
                        from a 'countData' object
